Nancy Black was charged in San Jose federal court Wednesday with committing the violations in 2004 and 2005 while operating her whale-watching business in Monterey Bay, the San Jose Mercury News reported.
The indictment alleges Black violated federal laws that prohibit a range of activities involving protected marine mammals in national marine sanctuaries such as Monterey Bay.
Black's alleged feeding, or attempted feeding, of whales could bring a rare prosecution under the Marine Mammal Protection Act.
Black's lawyers strongly defended her conduct.
San Francisco attorney Lawrence Biegel said at the time of the incidents Black had a research permit from the government and was within the law in conducting her research work.
"We view this indictment as an opportunity for Ms. Black to explain her techniques and methods to a fair-minded jury of her peers," Biegel said.